Greetings,
This sounds like an interesting application. I would suggest that you use your external pulse train as a scan clock, not as a start trigger. Furthermore, since you want to acquire data every third pulse, you will need to use one of your device's counters to divide-down this signal. To accomplish this task, you will need to configure the counter for pulse train generation with an external source - your external pulse train. You will then need to choose the correct "raw counts" to generate a pulse train with a frequency that is 1/3 of that of your external signal. I would suggest that you examine the example Generate Pulse Train (DAQ-STC).vi for this purpose. Now, you can perform a finite analog input acquisition of 2048 data points u
sing this pulse train as your scan clock. Finally, to determine the frequency of your scan clock, you will need to us your device's other counter to perform a frequency measurement of either pulse train.
I believe that this will be your best approach to accomplishing this task. Good luck with your application.
Spencer S.